RetrogeneDB ID: retro_cfam_1547

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 34:35409115..35409927(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ZCCHC9
• Ensembl ID: ENSCAFG00000008703
• Aliases: None
• Description: None

Sequence

>retro_cfam_1547
ATGACCAGGTGGGCACAAGTTACCACCACGCGTACCAAGAGACCTTTGGCTGCAACATCATGGGAAGACATGAAGAAGGG
GTCCTGTGAGGGAGAAAGCCAAAACCTACCAAAGAGTAAACAACTTGAAGCCAATAGGCTTTCTGTGAAAAATGATGCTC
CCAAAGCAAAACACAGAAAGGACAAAAAGAAAAAGGAGTATTTAAATGAAGATGTAAATGGATTCATGGAATACCTAAGA
GGAATCCACAGATGATTCACAATGGAGAGATGATAGCAACAGACAGTCAGGAGGTAAGGGAAGAAATTGCGGTTGCCTTA
AAGAAAGATAGCCGACGGGAAGGAAGAAGACTGAAAAGACAAGCAGCAAAGAAAAATGCAATGGTATGTTTCCATTGTAG
AAAACCTGGCCATGGGATTGCAGATTGCCCAGCTGCCCTTGAGAATCAAGATTTGGGCACTGGAATATGTTATTGCTGTG
GGTCCACAGAGCACGAAATAACCAAATGCAAAGCCAAAGTAGACCCAGCTCTTGGTGAATTTCCTTTTGCAAAATGTTTT
GTTTGTGGGGAAATGGGACATCTGTCCAGATCTTGTCCTGATAATCCCAAAGGACTCTATGCTGATGGTGGTTGCTGTAG
ACTTTGTGGCTCCGTGGAACACTTTAAGAAAGATTGCCCTGAGAGTCAAAATTCAGATCGAATGGTCACAGTTCGTCGCT
GGGGAAAGGGAATGAGTGCGGACTATGAAGAAATTTTGGATATGCCTAAACCACAGAAACCCAAAACAAAGATACCTAAA
GTTGTTAATTTT

Alignment

ORF - retro_cfam_1547 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.96 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTRWARVTTTRTKRPLAATSWEDMKKGSCEGESQNLPKSKQLEANRLSVKNDAPKAKHKKNKKKKEYLNE
          MTRWA.VTTTRTKRPLAATSWEDMKKGSCEGESQNLPKSKQLEANRLSVKNDAPKAKH.K.KKKKEYLNE
Retrocopy MTRWAQVTTTRTKRPLAATSWEDMKKGSCEGESQNLPKSKQLEANRLSVKNDAPKAKHRKDKKKKEYLNE

Parental  DVNGFMEYLR-QNPQMIHNGEMIATDSQEVREEIAIALKKDSRREGRRLKRQAAKKNAMVCFHCRKPGHG
          DVNGFMEYLR..NPQMIHNGEMIATDSQEVREEIA.ALKKDSRREGRRLKRQAAKKNAMVCFHCRKPGHG
Retrocopy DVNGFMEYLR<RNPQMIHNGEMIATDSQEVREEIAVALKKDSRREGRRLKRQAAKKNAMVCFHCRKPGHG

Parental  IADCPAALENQDMGTGICYRCGSTEHEITKCKAKVDPALGEFPFAKCFVCGEMGHLSRSCPDNPKGLYAD
          IADCPAALENQD.GTGICY.CGSTEHEITKCKAKVDPALGEFPFAKCFVCGEMGHLSRSCPDNPKGLYAD
Retrocopy IADCPAALENQDLGTGICYCCGSTEHEITKCKAKVDPALGEFPFAKCFVCGEMGHLSRSCPDNPKGLYAD

Parental  GGCCRLCGSVEHFKKDCPESQNSDRMVTVGRWAKGMSADYEEILDVPKPQKPKTKIPKVVNF
          GGCCRLCGSVEHFKKDCPESQNSDRMVTV.RW.KGMSADYEEILD.PKPQKPKTKIPKVVNF
Retrocopy GGCCRLCGSVEHFKKDCPESQNSDRMVTVRRWGKGMSADYEEILDMPKPQKPKTKIPKVVNF

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	0.04 RPM	5.42 RPM
SRP017611_brain	0.00 RPM	3.02 RPM
SRP017611_kidney	0.00 RPM	7.99 RPM
SRP017611_liver	0.36 RPM	4.64 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1547 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1547 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1547 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005265	1 retrocopy	retro_btau_1095,
Canis familiaris	ENSCAFG00000008703	2 retrocopies	retro_cfam_1547 , retro_cfam_675,
Choloepus hoffmanni	ENSCHOG00000005268	3 retrocopies	retro_chof_140, retro_chof_2143, retro_chof_268,
Callithrix jacchus	ENSCJAG00000019486	4 retrocopies	retro_cjac_1236, retro_cjac_2906, retro_cjac_3528, retro_cjac_909,
Echinops telfairi	ENSETEG00000003838	2 retrocopies	retro_etel_325, retro_etel_880,
Homo sapiens	ENSG00000131732	1 retrocopy	retro_hsap_1799,
Gorilla gorilla	ENSGGOG00000013790	1 retrocopy	retro_ggor_706,
Microcebus murinus	ENSMICG00000016266	5 retrocopies	retro_mmur_125, retro_mmur_1325, retro_mmur_1341, retro_mmur_606, retro_mmur_819,
Myotis lucifugus	ENSMLUG00000001886	1 retrocopy	retro_mluc_799,
Macaca mulatta	ENSMMUG00000020655	1 retrocopy	retro_mmul_797,
Mus musculus	ENSMUSG00000021621	1 retrocopy	retro_mmus_1920,
Otolemur garnettii	ENSOGAG00000002543	6 retrocopies	retro_ogar_1467, retro_ogar_2125, retro_ogar_2426, retro_ogar_2941, retro_ogar_3076, retro_ogar_459,
Pongo abelii	ENSPPYG00000015604	1 retrocopy	retro_pabe_1476,
Pan troglodytes	ENSPTRG00000017047	2 retrocopies	retro_ptro_1205, retro_ptro_602,
Rattus norvegicus	ENSRNOG00000014927	2 retrocopies	retro_rnor_1164, retro_rnor_2160,
Sorex araneus	ENSSARG00000008580	2 retrocopies	retro_sara_216, retro_sara_78,
Sarcophilus harrisii	ENSSHAG00000014504	1 retrocopy	retro_shar_734,
Ictidomys tridecemlineatus	ENSSTOG00000001407	2 retrocopies	retro_itri_422, retro_itri_696,
Tarsius syrichta	ENSTSYG00000012423	1 retrocopy	retro_tsyr_244,
Tursiops truncatus	ENSTTRG00000013796	1 retrocopy	retro_ttru_819,